Contents

1 Introduction

Matter 2 provides an updated and more robust C++ backend to matter objects, along with a completely new implementation of sparse arrays and new signal processing functions for nonuniform sparse signal data.

Originally designed as a backend for the Cardinal package, The first version of Matter was constantly evolving to handle the ever-increasing demands of larger-than-memory mass spectrometry (MS) imaging experiments. While it was designed to be flexible from a user’s point-of-view to handle a wide array for file structures beyond the niche of MS imaging, its codebase was becoming increasingly difficult to maintain and update.

Matter 2 was re-written from the ground up to simplify some features that were rarely needed in practice and to provide a more robust and future-proof codebase for further improvement.

2 Installation

Matter can be installed via the BiocManager package.

install.packages("BiocManager")
BiocManager::install("matter")

The same function can be used to update Matter and other Bioconductor packages.

Once installed, Matter can be loaded with library():

library(matter)

3 Usage

Coming soon…..

Coming soon…..

Coming soon…..

4 Session information

sessionInfo()
## R Under development (unstable) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] matter_2.1.0        Matrix_1.5-1        BiocParallel_1.33.0
## [4] BiocStyle_2.27.0   
## 
## loaded via a namespace (and not attached):
##  [1] cli_3.4.1           knitr_1.40          rlang_1.0.6        
##  [4] xfun_0.34           ProtGenerics_1.31.0 DBI_1.1.3          
##  [7] stringi_1.7.8       jsonlite_1.8.3      htmltools_0.5.3    
## [10] sass_0.4.2          rmarkdown_2.17      grid_4.3.0         
## [13] evaluate_0.17       jquerylib_0.1.4     fastmap_1.1.0      
## [16] yaml_2.3.6          bookdown_0.29       BiocManager_1.30.19
## [19] stringr_1.4.1       compiler_4.3.0      codetools_0.2-18   
## [22] irlba_2.3.5.1       lattice_0.20-45     digest_0.6.30      
## [25] R6_2.5.1            parallel_4.3.0      magrittr_2.0.3     
## [28] bslib_0.4.0         tools_4.3.0         biglm_0.9-2.1      
## [31] BiocGenerics_0.45.0 cachem_1.0.6